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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Pipeline version
        v1.0.0
        Contact E-mail
        qtl7@cdc.gov
        Project Type
        HMAS tripod analysis

        Report generated on 2024-09-06, 20:07 EDT based on data in:

        quast_report

        Assembly Statistics using Quast.

        Showing 80/80 rows and 4/4 columns.
        Sample NameN50 (Kbp)# of contigs >= 1KbpLargest contig (Kbp)Length (Kbp)
        CIMS-MN-055-SH-M-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-055-SH-K-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-051-IW-M-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-051-IW-K-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-053-SH-K-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-068-IW-M-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-053-IW-K-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-068-IW-K-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-069-SH-K-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-058-SH-K-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-050-IW-M-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-056-IW-M-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-050-SH-M-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-056-IW-K-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-065-IW-M-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-069-IW-K-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-064-IW-M-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-069-SH-M-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-065-SH-M-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-056-SH-K-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-049-SH-K-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-049-IW-K-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-049-SH-M-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-070-SH-K-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-070-IW-K-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-062-SH-M-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-062-IW-K-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-057-IW-M-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-054-SH-K-E_assembled
        396.0
        		27
        659.2
        		4660.0
        CIMS-MN-061-IW-K-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-061-IW-M-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-059-IW-K-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-051-SH-K-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-058-IW-K-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-064-SH-M-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-051-SH-M-E_assembled
        433.3
        		21
        947.7
        		4663.0
        CIMS-MN-058-SH-M-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-058-IW-M-E_assembled
        561.2
        		21
        815.6
        		4714.6
        CIMS-MN-065-SH-K-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-064-IW-K-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-063-SH-K-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-053-IW-M-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-057-SH-M-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-057-IW-K-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-054-SH-M-E_assembled
        396.0
        		27
        659.2
        		4660.0
        CIMS-MN-060-SH-K-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-068-SH-M-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-055-IW-K-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-064-SH-K-E_assembled
        479.0
        		23
        938.4
        		4738.6
        CIMS-MN-070-SH-M-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-049-IW-M-E_assembled
        496.7
        		25
        1462.3
        		4788.4
        CIMS-MN-063-SH-M-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-060-IW-M-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-070-IW-M-E_assembled
        370.5
        		25
        1076.6
        		4685.7
        CIMS-MN-067-IW-M-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-062-SH-K-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-054-IW-M-E_assembled
        396.0
        		27
        659.2
        		4660.0
        CIMS-MN-060-IW-K-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-059-SH-K-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-059-IW-M-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-062-IW-M-E_assembled
        479.2
        		21
        1508.5
        		4705.7
        CIMS-MN-056-SH-M-E_assembled
        434.4
        		23
        651.0
        		4823.7
        CIMS-MN-063-IW-K-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-061-SH-M-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-055-IW-M-E_assembled
        282.8
        		49
        821.2
        		5038.7
        CIMS-MN-059-SH-M-E_assembled
        490.5
        		20
        1508.5
        		4705.4
        CIMS-MN-067-IW-K-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-060-SH-M-E_assembled
        376.8
        		32
        591.0
        		4916.5
        CIMS-MN-050-SH-K-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-053-SH-M-E_assembled
        490.5
        		21
        1508.5
        		4738.2
        CIMS-MN-065-IW-K-E_assembled
        762.6
        		17
        2005.4
        		4712.3
        CIMS-MN-069-IW-M-E_assembled
        729.1
        		23
        1284.5
        		4937.2
        CIMS-MN-067-SH-K-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-067-SH-M-E_assembled
        490.3
        		20
        1508.5
        		4702.8
        CIMS-MN-050-IW-K-E_assembled
        146.8
        		63
        396.3
        		5187.5
        CIMS-MN-068-SH-K-E_assembled
        186.0
        		59
        514.5
        		5045.0
        CIMS-MN-063-IW-M-E_assembled
        762.6
        		15
        2004.8
        		4711.1
        CIMS-MN-057-SH-K-E_assembled
        440.5
        		25
        1195.4
        		4655.9
        CIMS-MN-061-SH-K-E_assembled
        320.2
        		44
        820.8
        		4896.5
        CIMS-MN-054-IW-K-E_assembled
        396.0
        		27
        659.2
        		4660.0

        tripod report

        Combined summary statistics for all the samples in the run, primer pairs (out of total 2461 in the Salmonella HMAS primer panel).

        Showing 47/47 rows and 4/4 columns.
        Sample Name# of FP# of not ident seqs# of matched most abund. seqs% of matched most abund. seqs
        CIMS-MN-056-SH-M-N-MN-M05688-240322940 301 / 3500.860
        CIMS-MN-052-SH-M-N-MN-M05688-24032240 0 / 40.000
        CIMS-MN-049-SH-M-N-MN-M05688-240322257 5 / 640.078
        CIMS-MN-056-SH-K-N-MN-M05688-2403221848 561 / 6270.895
        CIMS-MN-050-SH-M-N-MN-M05688-240322133 0 / 340.000
        CIMS-MN-049-SH-K-N-MN-M05688-240322170 14 / 850.165
        CIMS-MN-059-SH-K-N-MN-M05688-2403222433 686 / 7430.923
        CIMS-MN-054-SH-K-N-MN-M05688-24032210642 2163 / 23110.936
        CIMS-MN-058-SH-K-N-MN-M05688-24032211523 2194 / 23320.941
        CIMS-MN-052-SH-K-N-MN-M05688-24032270 0 / 70.000
        CIMS-MN-053-SH-K-N-MN-M05688-24032210922 2260 / 23910.945
        CIMS-MN-054-SH-M-N-MN-M05688-24032211154 2223 / 23880.931
        CIMS-MN-058-SH-M-N-MN-M05688-24032211420 2223 / 23570.943
        CIMS-MN-057-SH-K-N-MN-M05688-2403222783 832 / 9420.883
        CIMS-MN-050-SH-K-N-MN-M05688-240322346 2 / 510.039
        CIMS-MN-059-SH-M-N-MN-M05688-2403222026 441 / 4870.906
        CIMS-MN-061-SH-K-N-MN-M05688-240322440 110 / 1540.714
        CIMS-MN-060-SH-M-N-MN-M05688-24032200 1 / 11.000
        CIMS-MN-064-SH-K-N-MN-M05688-24032210343 2148 / 22940.936
        CIMS-MN-062-SH-M-N-MN-M05688-2403224994 1227 / 13700.896
        CIMS-MN-065-SH-K-N-MN-M05688-2403223428 965 / 10270.940
        CIMS-MN-057-SH-M-N-MN-M05688-2403222550 670 / 7450.899
        CIMS-MN-061-SH-M-N-MN-M05688-240322442 68 / 1140.596
        CIMS-MN-053-SH-M-N-MN-M05688-24032211020 2274 / 24040.946
        CIMS-MN-065-SH-M-N-MN-M05688-2403225838 1473 / 15690.939
        CIMS-MN-060-SH-K-N-MN-M05688-24032211016 2288 / 24140.948
        CIMS-MN-062-SH-K-N-MN-M05688-2403222561 444 / 5300.838
        CIMS-MN-068-SH-K-N-MN-M05688-2403223963 1012 / 11140.908
        CIMS-MN-076-MN-M05688-24032210 0 / 10.000
        CIMS-MN-066-SH-K-N-MN-M05688-24032223500 0 / 23500.000
        CIMS-MN-070-SH-K-N-MN-M05688-2403225951 1485 / 15950.931
        CIMS-MN-051-SH-K-N-MN-M05688-24032211514 2305 / 24340.947
        CIMS-MN-068-SH-M-N-MN-M05688-2403226255 1599 / 17160.932
        CIMS-MN-064-SH-M-N-MN-M05688-24032211233 2286 / 24310.940
        CIMS-MN-051-SH-M-N-MN-M05688-24032211615 2305 / 24360.946
        CIMS-MN-066-SH-M-N-MN-M05688-24032223660 0 / 23660.000
        CIMS-MN-075-SH-K-N-MN-M05688-24032260 0 / 60.000
        CIMS-MN-070-SH-M-N-MN-M05688-2403229560 2041 / 21960.929
        CIMS-MN-067-SH-K-N-MN-M05688-24032211218 2271 / 24010.946
        CIMS-MN-067-SH-M-N-MN-M05688-24032211219 2299 / 24300.946
        CIMS-MN-069-SH-K-N-MN-M05688-24032211820 2284 / 24220.943
        CIMS-MN-069-SH-M-N-MN-M05688-24032211819 2299 / 24360.944
        CIMS-MN-055-SH-M-N-MN-M05688-24032211316 2319 / 24480.947
        CIMS-MN-063-SH-M-N-MN-M05688-24032211417 2317 / 24480.946
        CIMS-MN-063-SH-K-N-MN-M05688-24032211320 2314 / 24470.946
        CIMS-MN-055-SH-K-N-MN-M05688-24032211416 2318 / 24480.947
        CIMS-MN-078-IH-MN-M05688-24032224520 0 / 24520.000

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